That's not quite right, at least judging by the books. The Protomolecule itself is just a machine with no self awareness whatsoever. It doesn't think at all, unlike the Borg. However, it doesn't really ever dispose of any information - which includes the consciousnesses of everyone absorbed on Eros. Thus their minds are in storage, still aware of existing, but trapped and having awful things done to them, not out of malevolence, just ignorance.